Library
library(plotly)
library(SummarizedExperiment)
Data
load("./input/atac_diff_chromatin_accessibility.RData")
load("./input/limma_SC_Controls.RData")
dea <- dea.limma$`PND15 vs Adult`
anno <- data.frame(data@metadata$annotation@anno, stringsAsFactors = F)
dar <- data.frame(rowData(data), stringsAsFactors = F)[, -c(2:6)]
dar <- merge(anno, dar, all.y = TRUE)
Map with Genes
dea.map <- dea[abs(dea$logFC) >= 1 & dea$adj.P.Val <= 0.05, ]
colnames(dea.map)[2:ncol(dea.map)] <- paste("DEA", colnames(dea.map)[2:ncol(dea.map)], sep = "_")
dar.map <- dar[abs(dar$logFC) >= 1 & dar$qvalue <= 0.05, ]
tab <- merge(dar.map, dea.map, by.x = "SYMBOL", by.y = "Genes")
tab.promoter <- tab[tab$annotation == "Promoter", ]
Save table
writexl::write_xlsx(tab, "./output/dea_genes_mapped_to_diff_acc.xlsx", col_names = T, format_headers = T)
SessionInfo
## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 3.6.1 (2019-07-05)
## os Ubuntu 16.04.6 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Europe/Zurich
## date 2019-11-29
##
## ─ Packages ───────────────────────────────────────────────────────────────────
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## promises 1.1.0 2019-10-04 [1]
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## questionr 0.7.0 2018-11-26 [1]
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## RCurl 1.95-4.12 2019-03-04 [1]
## remotes 2.1.0 2019-06-24 [1]
## rlang 0.4.2 2019-11-23 [1]
## rmarkdown 1.17 2019-11-13 [1]
## rmdformats 0.3.5 2019-02-19 [1]
## rprojroot 1.3-2 2018-01-03 [1]
## rstudioapi 0.10 2019-03-19 [1]
## S4Vectors * 0.24.0 2019-10-29 [1]
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